Mohadeseh S Tahami, Carlos Vargas-Chavez, Noora Poikela, Marta Coronado-Zamora, Josefa González, Maaria Kankare
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In this work, we used Drosophila montana as a model for cold-adapted organisms to study the association between TEs and adaptation to harsh climates.</p><p><strong>Results: </strong>Using the PacBio long-read sequencing technique, we de novo identified and manually curated TE sequences in five Drosophila montana genomes from eco-geographically distinct populations. We identified 489 new TE consensus sequences which represented 92% of the total TE consensus in D. montana. Overall, 11-13% of the D. montana genome is occupied by TEs, which as expected are non-randomly distributed across the genome. We identified five potentially active TE families, most of them from the retrotransposon class of TEs. Additionally, we found TEs present in the five analyzed genomes that were located nearby previously identified cold tolerant genes. Some of these TEs contain promoter elements and transcription binding sites. 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引用次数: 0
摘要
背景:上个世纪的重大发现揭示了转座元件(TEs)可通过影响基因表达和诱导基因重排等分子和结构效应在基因组进化中发挥关键作用。然而,我们对转座元件在适应极端气候方面所起作用的了解仍处于起步阶段。长线程测序技术的出现为更精确地识别和研究 TEs 的潜在功能效应提供了可能。在这项工作中,我们以果蝇作为寒冷适应生物的模型,研究了TEs与恶劣气候适应之间的关联:结果:利用 PacBio 长序列测序技术,我们从五个不同生态地理种群的果蝇基因组中重新鉴定并人工编辑了 TE 序列。我们鉴定出了 489 个新的 TE 共识序列,占蒙大拿果蝇总 TE 共识序列的 92%。总体而言,11%-13%的D. montana基因组被TE占据,正如预期的那样,TE在基因组中的分布是非随机的。我们发现了五个潜在的活性 TE 家族,其中大部分属于逆转录转座子类 TE。此外,我们还在五个分析的基因组中发现了位于先前发现的耐寒基因附近的TE。其中一些TE含有启动子元件和转录结合位点。最后,我们在固定和多态反转断点附近检测到了TE:我们的研究在蒙大拿果蝇的基因组中发现了大量新鉴定的TE共识序列,这表明应该对非模式物种进行研究,以全面了解果蝇及其他物种的TE谱系。利用新的蒙大拿果蝇基因库进行基因组注释,我们发现了位于耐寒基因附近的TEs,这些TEs以较高的种群频率存在,包含调控区域,因此是在蒙大拿果蝇冷应激反应中发挥作用的良好候选者。最后,我们的注释还让我们首次发现了存在于三个蒙大拿倒位基因断裂点的 TEs。
Transposable elements in Drosophila montana from harsh cold environments.
Background: Substantial discoveries during the past century have revealed that transposable elements (TEs) can play a crucial role in genome evolution by affecting gene expression and inducing genetic rearrangements, among other molecular and structural effects. Yet, our knowledge on the role of TEs in adaptation to extreme climates is still at its infancy. The availability of long-read sequencing has opened up the possibility to identify and study potential functional effects of TEs with higher precision. In this work, we used Drosophila montana as a model for cold-adapted organisms to study the association between TEs and adaptation to harsh climates.
Results: Using the PacBio long-read sequencing technique, we de novo identified and manually curated TE sequences in five Drosophila montana genomes from eco-geographically distinct populations. We identified 489 new TE consensus sequences which represented 92% of the total TE consensus in D. montana. Overall, 11-13% of the D. montana genome is occupied by TEs, which as expected are non-randomly distributed across the genome. We identified five potentially active TE families, most of them from the retrotransposon class of TEs. Additionally, we found TEs present in the five analyzed genomes that were located nearby previously identified cold tolerant genes. Some of these TEs contain promoter elements and transcription binding sites. Finally, we detected TEs nearby fixed and polymorphic inversion breakpoints.
Conclusions: Our research revealed a significant number of newly identified TE consensus sequences in the genome of D. montana, suggesting that non-model species should be studied to get a comprehensive view of the TE repertoire in Drosophila species and beyond. Genome annotations with the new D. montana library allowed us to identify TEs located nearby cold tolerant genes, and present at high population frequencies, that contain regulatory regions and are thus good candidates to play a role in D. montana cold stress response. Finally, our annotations also allow us to identify for the first time TEs present in the breakpoints of three D. montana inversions.
期刊介绍:
Mobile DNA is an online, peer-reviewed, open access journal that publishes articles providing novel insights into DNA rearrangements in all organisms, ranging from transposition and other types of recombination mechanisms to patterns and processes of mobile element and host genome evolution. In addition, the journal will consider articles on the utility of mobile genetic elements in biotechnological methods and protocols.